--- MITgcm/doc/tag-index	2011/03/15 00:25:14	1.1397
+++ MITgcm/doc/tag-index	2012/02/13 23:45:41	1.1596
@@ -1,9 +1,1143 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1397 2011/03/15 00:25:14 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1596 2012/02/13 23:45:41 gforget Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice : 
+  - simplify McPhee tapering, and allow to use it with SEAICEturbFluxFormula.EQ.
+  1 or 2, using newly added run time parameter SEAICE_availHeatTaper.
+  - fix d_AREAbyATM, d_AREAbyOCN, d_AREAbyICE diags I broke in r1.148.
+  - add permanent SItflux diag that corresponds to TFLUX but includes 
+  ice+snow. Hence SItflux-TFLUX should match the ice+snow heat budget.
+  - allow activation/testing of a fix for suspected missing term in 
+  ocn-ice heat budget (to be confirmed). To test this, you want to 
+  undef SEAICE_DISABLE_HEATCONSFIX, and then set the run time param
+  SEAICEheatConsFix to .TRUE. that also allows the 'SIaaflux' diagnostic.
+  - no change in results, fwd or ad.
+o global_ocean.cs32x15/results: three changes following from the pkg/seaice commit below.
+  - switch to variable freezing point. 
+       Results change : cg2d -> 1 digits; ad -> 3-6-6 digits.
+  - bug fix : the sublimation term that was missing is now activated.
+       Results change : cg2d -> 2 digits; ad -> 8-6-6 digits.
+  - bug fix : flooding sign term for SIsal0.NE.0. 
+       Result change : cg2d -> 8 digits; ad -> 11-12-9 digits.
+o pkg/seaice:
+  - unified freezing point treatment : the old SEAICE_VARIABLE_FREEZING_POINT
+ is now the default, and the old default constant freezing point is recovered with 
+ SEAICE_tempFrz0    = -1.96,
+ SEAICE_dTempFrz_dS = 0.,
+  - retire SEAICE_freeze that was the old way of specifycing the constant freezing point.
+  - remove ALLOW_SEAICE_FLOODING brackets; run time switch is already there.
+  - bug fix (thanks to M. Losch) : the sublimation term that was missing is now 
+ activated. To reproduce old results that had this bug define SEAICE_DISABLE_SUBLIM.
+  - bug fix (silly me) : flooding sign term (seaice_growth.F r 1.149line 1211) 
+ was wrong for SIsal0.NE.0. Changes cs32x15 results (see above item for detail).
+  - bug fix (thanks to O. Jahn) : area loss for melting  got messed up in 
+ seaice_growth r149 for legacy branch (no results change).
+  - introduce SEAICE_CAP_SUBLIM : caps sublimation heat flux in solve4temp (code from I. Fenty).
+  - results did not change except for global_ocean.cs32x15, mostly due to the switch 
+  to variable freezing point (see above item for detail).
+o pkg/thsice:
+  - fix and simplify interface to salt_plume pkg ; diagnose directly amount of
+    seawater freezing in thsice_calc_thickn (not used).
+o pkg/seaice: turbulent flux term specification via run time params.
+  - replace CPP switches with run time switches to facilitate testing
+  - retired CPPs : MCPHEE_OCEAN_ICE_HEAT_FLUX, GRADIENT_MIXED_LAYER_TURBULENCE_FACTOR
+  - added runtime parameter : SEAICEturbFluxFormula
+  - move Mcphee constants to SEAICE_PARAMS.h
+  - seaice_readparms.F : read turbulent flux term params (SEAICEturbFluxFormula;
+    SEAICE_availHeatFrac/Frz, or SEAICE_gamma_t/_frz if apply); remove
+    seaice_summary call (moved to seaice_init_fixed)
+  - seaice_init_fixed.F : set SEAICE_availHeatFrac/Frz depending on
+    SEAICEturbFluxFormula, and seaice_summary call (moved from seaice_readparms)
+  - seaice_summary.F : add missing report of read turbulent flux term set up (and SITRACER).
+  - seaice_check.F : check range; inform and stop if retired CPPs are used (incl. SEAICE_AGE).
+  - seaice_growth.F : unified use of SEAICE_availHeatFrac/Frz, without
+	CPP switch, same computation as before for the different options.
+  - change results at the truncation level.
+o pkg/seaice:
+  - remove un-used parameters LAD & MAX_TICE ; add new run-time parameters:
+    useMaykutSatVapPoly (default=F), postSolvTempIter (default=2) and
+    SEAICE_wetAlbTemp (default=-1e-3). Remove option SEAICE_SOLVE4TEMP_LEGACY.
+  - update verification/*/input*/data.seaice:
+    to reproduce previous results with former #defined SEAICE_SOLVE4TEMP_LEGACY
+    code, set useMaykutSatVapPoly=T & postSolvTempIter=0 ;
+    and to reproduce previous results with former non-SOLVE4TEMP_LEGACY code,
+    set SEAICE_wetAlbTemp=0 & SEAICE_snowThick=0.
+o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY):
+  - remove LEGACY code for solving for tsurf (A1,A2,A3) but maintain the same
+    algorithm (same choice: useMaykutPolySatVap=T, postSolvTempIter=0);
+    difference in results only due to machine truncation.
+  - remove MAX_TICE (tsurf is always =< TMELT anyway); keep MIN_TICE if using
+    MaykutPolySatVap; keep MIN_LWDOWN.
+  - adapt SEAICE_MODIFY_GROWTH_ADJ code (untested) to non-legacy formulation.
+  - update output of verification exp. lab_sea (4 fwd: 11 cg2d digits except hb87,
+    + 3 AD: 6 digits except evp) and offline_exf_seaice.seaice (12 digits).
+o pkg/salt_plume:
+  - isolate saltPlumeFlux array exch into a specific S/R called from
+    do_oceanic_phys.F
+  - add interface to pkg/salt_plume (filling of saltPlumeFlux) in pkg/thsice.
+o verification:
+  - move untested set-up to MITgcm_contrib/verification_other.
+o pkg/seaice:
+  - retire old way of SEAICE_AGE. Now replaced with ALLOW_SITRACER.
+o pkg/seaice:
+  - seaice_solve4temp.F (keeping results unchanged):
+    * add 2 future run-time params to select which saturation vapor pressure
+      formula is used and how post-iteration fluxes are set.
+      Temporary set these 2 params according to option SOLVE4TEMP_LEGACY;
+    * New piece of code (not used) to update surf. atmos. heat flux F_ia using
+      the linearized expression to stay consistent with tsurf finding.
+  - seaice_freedrift.F avoid floating exception in sqrt(y) since y=sqrt(x*x)-x
+    can be < 0.
+o pkg/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
+  - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
+    conductive heat flux F_c , and add it explicitly when updating tsurf as
+    solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
+    so that now F_ia has a consistent meaning through the entire routine.
+    This causes differences at truncation level: update output of fwd exp.
+    global_ocean.cs32x15.seaice.
+o pkg/seaice:
+  - lots of editing/cleaning in seaice_solve4temp.F + better documentation
+    of arrays, sign/direction of fluxes; no effect on results.
+  - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
+    in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
+    note: this should have been done before changing celsius2K default.
+  - to keep results unchanged, add back old value of celsius2K in verification
+    exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
+  - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
+    SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
+    value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
+    freezing temp is consistent with value in seaice_growth.F ; this causes
+    differences at machine truncation level: update lab_sea AD output (3/4).
+o pkg/seaice:
+  - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
+    and climsst/sss even when using seaice (to prevent calculation that might
+    use SST on land); does not affect any verification exp.
+  - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
+    of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
+o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
+  over land (non-legacy code)
+o vectorize salt_plume package:
+  - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
+  - this code computes plumebk everywhere (also over land), thus requires
+    code to avoid divisions by zero and catch the case of kLev=Nr.
+  - efficiency of salt_plume_frac is still sub-optimal
+o tools (genmake2):
+  - fix makefile NAME specification (option: -makefile NAME) by adding
+    "-f $MAKEFILE" in few places where it was missing including makedepend
+    command (contribution from Paul).
+
+checkpoint63i (2012/01/24)
+o model/src:
+  - add factorized versions of some EOS code to find_rho.F,
+    define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
+o model/src:
+  - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
+  - change default celsius2K from 273.16 to 273.15
+  - to keep results unchanged, add back old value of celsius2K in verification
+    exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
+     global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
+o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
+  to make TAF generate vectorizable code
+o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
+   Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
+   have flags that do this more efficiently.
+o pkg/diagnostics/diagstats_calc.F
+  - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
+o pkg/obcs (with exch2):
+  - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
+    and remove code (in obcs_readparms.F) which was based on EXCH of indices
+    (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
+o pkg/exf and seaice exp:
+  - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
+    so that switching off area & heff advection flags does not affect results.
+  - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
+  - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
+    EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
+    results of verification experiments: 1D_ocean_ice_column(fwd),
+    global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
+    and offline_exf_seaice (all 4).
+o pkg/seaice:
+  - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
+    remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
+  - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
+    but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
+    not multi-dim advection;
+  - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
+    SHORTWAVE_HEATING #undef.
+o optim: make Makefile more robust (?)
+o pkg/obcs:
+  * fix treatment of obcs_read_pickup for TAF
+o pkg/shelfice:
+  * add missing initialisation of num_shifwflx
+  * new adjoint verification exp. for isomip
+  * change Prandtl and Schmidt numbers from generic formulations
+    (in terms of model diffus. and visc.) to separate runtime
+    parameters, with Holland and Jenkins (1999) default values.
+o pkg/exf (interpolation):
+  - extended input field (2 rows) near the N & S poles:
+    * fill in with the symetric value (when even Nb of data in longitude)
+    * add average value at the poles only for scalar quantities ; for vector
+      component interpolation, skip the averaging and keep duplicated values,
+      unless the 2 components have same location (uvInterp=T) in which case
+      interpolate the 2 components together using S/R EXF_INTERP_UV.
+  - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
+    together: this allows to account properly for local orientation when
+    averaging at N & S pole.
+  - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
+    exf-interpolation near N & S poles. Undef by default.
+  - add debug check/print on 1rst iter if debugLevel >=2.
+o pkg/exf:
+  - change masking flags definition (no longer "parameter"), put them in
+    common block and set them in S/R EXF_INIT_FIXED.
+  - change recognized masking flag from s,u,v to c,w,s since the mask
+    to use (maskC,W,S) depends on position on model grid and has little to
+    do with scalar/vector difference; fix masking if using P-coordinates.
+  - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
+    and update results of exp. global_with_exf (x2).
+  - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
+o pkg/obcs
+  - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
+o pkg/exf (interpolation):
+  - assume periodicity in X only if input field cover full longitude range.
+  - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
+    and should vectorise).
+  - fix input lat of the 2 added row (in case we provide N.pole data).
+
+checkpoint63h (2011/12/30)
+o pkg/seaice:
+  - change declaration of UVM from _RL to _RS in order to get B-grid
+    uIce,vIce monitor when _RS = real*4
+o pkg/offline:
+  - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
+  - compute vertical velocity if not read from file (switch on exactConserv
+    & staggerTimeStep);
+  - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
+o verification:
+  - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
+    with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
+    fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
+  - update output of exp. global_ocean.cs32x15.viscA4 after changing
+    grid-file angles (used here for coriolis-3d);
+  - remove (or gzip) few files not needed to run fizhi-cs experiments.
+o pkg/exf (vector interpolation):
+  - rotate vector component toward local grid-axis orientation using grid-angles
+    (stored in GRID.h) instead of locally computed rotation angle; keep old code
+    available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
+o pkg/seaice:
+  - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
+    undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
+o pkg/PKG_OPTIONS.h files:
+  - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
+    outside of the #ifdef ALLOW_THISPKG / #endif block.
+  - update verification/*/code/PKG_OPTIONS.h files.
+o add a verification experiment (offline_exf_seaice/input.seaice) that test
+  the B-grid LSOR solver
+o pkg/seaice: sort out emissivity and long wave radiation step 2:
+  - add emissivity for snow and ice as new run-time parameters
+    (unfortunately) that default to the corresponding exf values; this
+    changes results in most verification experiments so that for backward
+    compatibility these parameter have to be set explicitly to inconsistent
+    values (ugly);
+  - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
+    emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
+    until we agree how to handle this bug properly
+o pkg/exf (interpolation):
+  - add a set of run-time param ({inputfield}_interpMethod), one for
+    each interpolated input field, to select the interpolation method
+    with a value of zero switching off the interpolation;
+  - print interpolation parameters to standard output;
+  - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
+    (to use instead runoff_interpMethod=0 in data.exf).
+  - simplify default setting of interpolation parameters (for all fields,
+    set position to match model grid cell-center position, leading to trivial
+    interpolation in case of regular Lat-Lon grid) and fix for the case of
+    non-uniform delY.
+o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
+   within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
+   this factor is absolutely required, because the lw exitance (= out-going
+   long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
+   where the reflectivity rho = 1-emissivity for conservation reasons. Once
+   this is established, we can remove the CPP-Flag (if we want to).
+o pkg/seaice:
+  - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
+    ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
+  - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
+    what the name implies (and not emissivity*BoltzmannConstant), this means
+    the old default value of 5.5e-8 now means
+    5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
+    S/R exf_readparms
+  - FV-discretization of the B-grid LSOR solver, turn on with
+    SEAICE_LSRBNEW. This new solver also involves a slight re-organization
+    of the calling routine dynsolver, so that B and C-grid code look a
+    little more alike.
+  - fix index bugs in ostres.F (B-grid code)
+o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
+o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
+  default for SEAICE_emissivity, if useEXF; requires setting a wrong
+  parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
+  backward compatiblity
+o model/src: use sigmaR in calc_ivdc
+
+checkpoint63g (2011/12/16)
+o pkg/seaice/seaice_growth.F:
+  fix heat conservation of the coupled ocean-seaice system.
+  when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
+  solid vs liquid water treatment is resolved via QNET.
+o pkg/seaice/seaice_growth.F:
+  add missing term for sublimation in saltFlux, which was breaking conservation.
+o pkg/seaice/seaice_model.F:
+  Remove this patholigical case treatment in evolution branch,
+  where it is un-necessary and breaks conservation.
+  Update global_ocean.cs32x15/results accordingly for
+  output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
+o model/src:
+  useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
+  external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
+o pkg/obcs:
+  modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
+  tendency for temperature and salinity that is then applied to update
+  theta and salt in S/R obcs_apply_ts; this requires proper masking of all
+  horizontal advection and diffusion contributions on the boundary (in
+  S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
+  removing the mask in S/R timestep_tracer. The advantage of this approach is
+  that the updated tracer values include contributions from the surface
+  forcing and vertical diffusion.
+  This modification changes exp4.stevens because of vertical diffusion.
+o model/src:
+  change non-curvilinear grid setting to also work with exch2 + blank tiles:
+  - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
+    face dimensions.
+  - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
+    as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
+    and INI_SPHERICAL_POLAR_GRID.
+  change test-experiment global_ocean.90x40x15:
+  - split the domain in many more tiles (9x4 tiles of 10x10 each);
+  - switch to exch2 and remove 1 blank-tile (but only for MPI test).
+  - update results of both test (std & dwnslp).
+o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
+   tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
+o model/src:
+  - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
+    and fix initialisation when using sigma-coords.
+o model/src:
+ - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
+   to their current value at the beginning of forward_step.F": add a new run-time
+   switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
+ - set doResetHFactors=T in the following test exp:
+    global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
+    global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
+    and tutorial_global_oce_in_p (nonLinFS in p)
+o pkg/ecco
+  - added IES cost term
+o verification/advect_xz
+  - scale down the depth by 1/100 (from 200 km to just 2.km)
+  - add secondary test using divergent flow, r-star and implicit vertical advection.
+  - add note (check_conserve_TS.txt) and matlab script to check global
+    conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
+o pkg/rbcs:
+  - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
+o pkg/obcs (Stevens BCs):
+  - fix various problems in the phase speed computations of the Stevens
+    boundary conditions:
+    - sign error for western and southern boundaries,
+    - time tendencies were underestimated by factor of dTracerLev and some just
+      zero (for multidim advection schemes) -> now estimate time tendencies
+      from difference between previous (n) time level and the one before (n-1);
+      this requires storing a field per tracer per boundary, also in the pickup
+      files.
+    - replace deltaTmom in cflMer/Zon computation with dTracerLev
+    - set default phase velocity to cflMer/Zon
+  - update verification experiment exp4.stevens
+o pkg/generic_advdiff (implicit_r):
+  - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
+    (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
+  - fix implicit vertical diffusion or advection with NonLin FreeSurf
+    (was using current recip_hFacC instead of future recip_hFacC): set future
+    recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
+    solver S/R ;
+  - fill diagnostics of vertical advective fluxes (computed from tendency)
+    when using implicit vert. advection;
+  - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
+     global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
+     tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
+     and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
+o pkg/diagnostics:
+  - add diags for T & S tendency which goes through Adams-Bashforth.
+
+checkpoint63f (2011/11/30)
+o pkg/obcs/obcs_calc_stevens.F:
+  - join some loops to reduce number of if-statements
+  - fix a bug in code for northern and southern boundaries.
+o pkg/seaice/seaice_init_varia.F
+  - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
+    caused zero ice-velocities for the B-grid code
+o pkg/seaice/seaice_init_fixed.F
+  - fix a bug in the initialisation of the second metric terms
+    k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
+  - this affects all seaice configurations with useCurviLinearGrid = .true.
+    and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
+    = .true. (default)
+  - the only verification experiment affected is global_ocean.cs32x15:
+    icedyn, seaice, and seaice_dynmix (AD)
+o pkg/thsice/thsice_diagnostics_state.F
+  - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
+    not contain garbage that can lead to surprises in diagstats_calc.F
+o model/src:
+  - move bi,bj loops inside INTEGR_CONTINUITY ;
+  - call INTEGR_CONTINUITY directly from forward_step.F
+    (previously called from momentum_correction_step.F)
+  - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
+    forward_step.F and pkg/ecco/the_main_loop.F
+o model/src/do_oceanic_phys.F:
+  - reset addMass to zero only if useICEFRONT ;
+  - separated k-loop for rhoInSitu calculation ;
+  - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
+    and at constant T,S (= WdRHOdP);
+  NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
+    of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
+    transport of locally-referenced potential density);
+    to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
+o gluemnc:
+  - replace ncrcat with ncks when adding variables to *.glob.nc
+  - change the way variables without record dimensions are handled so that
+    files that have variables with and without record variables can be glued:
+    add a record dimension with a new unique name to be able to differentiate
+    between variable with and without a-prior record dimensions. Remove
+    this record dimension before adding the variable to the *.glob.nc file.
+    This procedure automatically works also for grid.*.nc files that do not
+    have any record dimension.
+o verification/cpl_aim+ocn:
+  - generate new reference output on baudelaire (gfortran, mpich2) (previously
+    from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
+o pkg/obcs/obcs_calc_stevens.F:
+  - add code for northern and southern boundaries.
+  - reorder some loops to save some operations and so that drFBar can be scalar
+o model/src:
+  - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
+    truncation) and add diagnostics for Adams-Bashforth tendency increment.
+  - update test-exp. AD output:
+    1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
+  and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
+    front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
+    global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
+    matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
+    tutorial_global_oce_in_p, tutorial_global_oce_latlon and
+    tutorial_plume_on_slope.
+o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
+  that vectorises. This code uses 3 extra 2D fields, F90 array assignments
+  and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
+  does not even come with an F77 compiler anymore, this should not be
+  a limitation
+
+checkpoint63e (2011/11/06)
+o pkg/seaice adjoint of LSR:
+  - substantially rework STORE dirs.
+  - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
+    this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
+    and only perform SOLV_MAX_FIXED adjoint iters.
+    If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
+    always goes to same record, meaning that the last forward field will be
+    the one used in the adjoint - an approximation.
+  - now produces non-zero LSR-related gradients, and acceptable gradients for
+    An's zonal (x-z) test case (to be checked in)
+  - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
+    (but these are screwed up by the thermodynamics in the first place);
+    reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
+    output_adm.txt also reflects changes to seaice_lsr
+  - global_ocean.cs32x15:
+    * the "default" input_ad.seaice has been re-defined to always exclude dynamics
+      (output_adm.seaice.txt was updated)
+    * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
+      (output_adm.seaice_dynmix.txt)
+o test-exp. exp4+stevens:
+  - switch off pTracers and nonHydrostatic (restart problems with NH); update output
+o pkg/seaice (lsr solver):
+  - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
+    update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
+  - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
+  - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
+    into initial guess for linearised solver; use weight ~ (1/err)^2,4.
+  - compute (with new S/R) and print initial (+ free-driff sol. if available)
+    and final residual of linearised system.
+o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
+  (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
+o pkg/obcs: Stevens BCs (still only for east and west)
+  - fix Stevens BCs by using intermediate velocities of previous
+    time step as "baroclinic" contribution rather velocity of one grid cell
+    inside the boundaries; more consistent but makes the entire treatment
+    more complicated, requires new pickup files and two new S/Rs:
+    obcs_copy_uv_n and obcs_save_uv_n
+    keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
+    (undefined by default)
+  - silently move computation of some grid factors into separate loops to
+    save some recomputations
+  - add a hack for non-linear free surface
+  - add a verification experiment to exp4 that tests this code
+o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
+
+checkpoint63d (2011/10/25)
+o pkg/obcs + seaice-dynamics:
+  - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
+    solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
+    values (consistent with an implicit method).
+  - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
+    return to older implementation (same results as before); note that none of
+    the "experimental" OBCS_SEAICE options are implemented in the new version.
+  - switch test exp. seaice_obcs to use new version (update output).
+o pkg/seaice:
+  - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
+  - add parenthesis in Water-Ice drag calculations (evp & lsr);
+  - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
+    and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
+  - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
+    and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
+o pkg/layers:
+  - Include potential density as new coordinate (Thanks to David Munday)
+o pkg/dic:
+  - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
+    carbonate computation/output to CALC_PCO2_APPROX
+o pkg/generic_advdiff
+  - make TAF generate code that vectorizes:
+    gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
+o model/src:
+  - improve vectorization also for adjoint code of
+    solve_tridiagonal and solve_pentadiagonal. As this requires up to
+    5 new 3D-fields, this code is only turned on for the combination of
+    ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
+    for singular matrix check (only for TARGET_NEC_SX).
+  - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
+    ALLOW_AUTODIFF. This flag now needs to be set outside of
+    solve_tri/pentadiagonal.F
+o pkg/exf:
+  - fix previous modif in exf_readparms.F (revision 1.66: treatment of
+    optional namelist EXF_NML_OBCS).
+  - add many debug-print (to trace down where pkg/cal error msg comes from)
+o pkg/mom_vecinv/mom_vi_hdissip.F
+  - rearrange loops so that vectorization is improved and in particular
+    the adjoint routine vectorizes. The code is a little longer now, but I
+    think easier to read.
+    Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
+o pkg/seaice:
+  - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
+o pkg/exch2:
+  - alternative code (without tile x tile matrix) for cumulated (global) sum;
+    used as default; keep using matrix version in adjustment.cs-32x32x1.
+o tools/build_options:
+  - after merging some MPI and/or multi-threads specific optfiles so that
+    the modified default optfile support both built (using genmake2 -mpi
+    for the MPI built, using genmake2 -omp for OpenMP built),
+    move now obsolete optfiles to tools/build_options/unsupported/
+   (add copy of email sent to support list in doc/optfiles_changes.txt)
+
+checkpoint63c (2011/09/28)
+o pkg/ebm:
+  - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
+    test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
+o pkg/seaice (SItracer pickup)
+* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
+  To be done:
+  - thorough testing of missing fields in S/R seaice_read_pickup
+  - thorough matching between generic tracers and specific fields used
+    (e.g. volume-weighted age, area-weighted age, salinity, ...)
+o pkg/grdchk:
+  - all procs calculate and print finite-difference gradient (for testreport)
+  - change description output used by testreport;
+  - AD testing: also compare and report Finite-difference gradient;
+    => update all output_adm*.txt
+o test exp. global_ocean_ebm:
+  - switch back useRealFreshWaterFlux (no problem anymore with run-off);
+    and turn on exactConserve; update (fwd) output.
+o pkg/seaice (LSR):
+  - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
+  - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
+    * identical results with non-CS topology (but save up to half of EXCH calls)
+    * no much changes in cs-32 verification tests since no ice at face edges
+     (differences due to convergence criteria, since nb of iterations changed)
+    * expect some differences on lat-lon-cap grid.
+    update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
+o pkg/exch2:
+  - add new CPP option to disable Cumul-Sum matrix (to save storage when using
+    many tiles); until alternative coding is added, just add a stop.
+o pkg/kpp:
+  - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
+    to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
+o optfiles:
+  - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
+    into corresponding standard one, which now support different build:
+    (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
+  - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
+o pkg/obcs (seaice):
+  - add missing EXCH for uIce,vIce after applying OBCS;
+  - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
+    argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
+    EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
+  - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
+  - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
+    and eedata.mth for MPI and mutlti-threaded testing.
+o pkg/flt:
+  - make FLT EXCH working with multi-threads (and MPI + multi-threads);
+  - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
+  - fix pickup and trajectories + profiles output with multi-threads;
+  - add parameter to select group of fields to write along trajectory and
+    profile (default unchanged);
+  - only call PORT_RAND* function when flt_noise <> 0;
+  - add multi-threaded test for verification exp. flt_example.
+o eesupp/src:
+  - fix S/R ALL_PROC_DIE for MPI+multi-threads.
+  - USE_OMP_THREADING: check that number of threads (from eedata) matches
+    actual number (from env.var. setting).
+o pkg/ebm:
+  - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
+  - add multi-threaded test for verification exp. global_ocean_ebm
+
+checkpoint63b (2011/08/29)
+o pkg/ebm:
+  - fix sign of runoff;
+  - update directly forcing fields (Qnet,EmPmR) to use standard
+    external_forcing_surf.F (remove ebm_forcing_surf.F);
+  - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
+  - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
+    and apply relaxation towards corresponding SST field (2-D map or ZonAver).
+  - update global_ocean_ebm parameters file data and update output (fwd+ad).
+o verification/matrix_example:
+  - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
+    MPI and mutlti-threaded testing.
+o pkg/matrix:
+  - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
+  - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
+  - fix for multi-threaded (remove DATA statement);
+  - use standard DIFFERENT_MULTIPLE function;
+  - add MATRIX_OPTIONS.h
+o verification/matrix_example:
+   To allow to split the domain in several tiles, change the domain size
+    from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
+    Western side) of land points.
+o (*_)write_pickup:
+  - fix few bugs in mypackage_read/write_pickup.F
+  - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
+    array of length 1 (was caught by compiler syntax-check).
+o pkg/diagnostics (velocity potential solver):
+  - fix initialisation of main diagonal matrix (for overlap values)
+o tools/build_options:
+  - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
+    into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
+  - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
+    * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
+    * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
+    and use "-devel" testreport option for standard testing on baudelaire.
+o pkg/grdchk:
+  - Assume that all gradient-check position are within the same tile
+    corresponding to global indices (iGloTile,jGloTile) and that
+    positions (i,j indices or nbeg) are local to this tile;
+  - set tile local-indices and proc. number according to tile global-indices;
+  - remove grdchkwhichproc from namelist (retired param);
+  - send adjoint gradient to all procs so that all procs print it to STDOUT;
+  - switch on MPI test for global_ocean.90x40x15 AD test experiment.
+o adding package bbl (Bottom Boundary Layer)
+  description in MITgcm/pkg/bbl/bbl_description.tex
+  example/test experiment in MITgcm_contrib/bbl
+o adjoint verifications
+  - changed 5 experiments to multi-tiles
+    * global_ocean.90x40x15
+    * obcs_ctrl
+    * offline_exf_seaice
+    * tutorial_dic_adjoffline
+    * tutorial_tracer_adjsens
+    changed reference output for those that crossed tile boundaries
+    (changed choices of gradient check positions)
+  - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
+  - temporary bug fix in grdchk_loc.F for obcs
+o genmake2 & testreport
+  - add target "obj" (just for OBJFILES files) to Makefile;
+  - add option to specify FEXTRAFLAGS on command line.
+o pkg/mypackage:
+  - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
+
+checkpoint63a (2011/08/02)
+o pkg/diagnostics (velocity potential):
+  - fix velocity-potential calculation when using OBCS: balance net inflow
+    at each level (new S/R OBCS_DIAG_BALANCE).
+  - fix some of the problems with OBCS in stream-function calculation.
+o pkg/exf/exf_readparms.F
+  - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
+    EXF_NML_OBCS) more consistent, so that you need not have these lists
+    in data.exf when they are not used.
+o optim/optim_readdata.F:
+  - add some output about obcs variables that might help debugging
+  - add a check about nvarlength
+o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
+o pkg/diagnostics (velocity potential):
+  - fix mask for OBCS (still problems in stream-function with OBCS);
+  - add specific parameter (default = main code CG2D params) for solver;
+  - in case of poor convergence, use solution corresponding to lowest residual.
+o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
+  adjoint code. In general statements like tmpscal=fld(i,j) are problematic
+  and should be avoided where possible.
+o model/src (rStar):
+  - include r* effect on reference-state (PhiRef) in totPhiHyd
+    (so that it's really the potential anomaly at the cell center);
+    affect solution only if z* with full pressure in EOS.
+  - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
+    update output (because of z* in totPhiHyd and viscA4 changes);
+  - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
+    @ constant r) until interpolation at constant r is implemented.
+o pkg/diagnostics
+  - fix RCENTER diagnostics in case cell center is not at interface middle
+o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
+  this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
+  that THETA and SALT are "conservative temperature" and "absolute
+  salinity"
+o pkg/ctrl
+  - fix computation of endrec in s/r ctrl_init_rec
+  - ctrl_pack/unpack_*: remove unused variables and some obsolete code
+o pkg/seaice/seaice_growth.F
+  - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
+    remove then obsolete STORE directives
+  - fix STORE directives for tice and tices, so that only the
+    appropriate part of the fields are stored (and not the entire
+    field); update global_ocean.cs32x15.seaice AD output.
+  - cosmetic changes: adjust CPP flags and indentation for better
+    legibilty
+o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
+  Chris Wilson)
+o pkg/gmredi:
+   Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
+   and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
+
+checkpoint63  (2011/07/11)
+o pkg/exch2:
+ - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
+ - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
+   (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
+   increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
+o pkg/diagnostics:
+ - deal with pairs of post-processed diags which are computed together; in
+   particular, re-order list of diags within 1 file to save 2nd computation.
+ - add S/R to compute velocity stream-function (called after velocity-potential
+   calculation) from divergence free transport -> new diagnostics "PsiVEL".
+ - add parameter to select grid-point location where PsiVEL == 0.
+o eesupp/src:
+   new S/R to calculate cumulated sum on tiled array, corner grid-cell location
+   (specific S/R needed with exch2 topology - for now, just print an error msg)
+o pkg/shelfice
+ - Implement friction velocity-dependent transfer coefficients following
+   Holland and Jenkins, JPO, 1999
+   Original code by M. Losch with small modifs.
+   Enable with CPP option SHI_ALLOW_GAMMAFRICT
+   and runtime flag SHELFICEuseGammaFrict
+o verification lab_sea & global_ocean.cs32x15:
+ - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
+   does not miss some dependencies (but is slower) and also works with many files
+   (default makedepend limitation for AD built).
+ - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
+o pkg/diagnostics:
+ - add run-time parameter "useMissingValue" (def=False) to fill land-point
+    (i.e., where mask=0) with MissingValue ; used only in MNC output file.
+   This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
+ - Extend the use of "missing_value" setting from data.diagnostics for the case
+   of counter-diagnostics (where fraction-weight is zero). This applies both to
+   MNC and MDS output files.
+o pkg/seaice/seaice_growth.F:
+  - add 'a priori' cap of latent heat flux based on actual mass considerations
+    when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
+    non-legacy seaice_solve4temp.
+  - add diagnostic of the residual sublimation freshwater flux (the freshwater
+    flux taken from the ocean if the total actual latent heat fluxes exceed
+    the maximum)
+  - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
+   fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
+  - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
+   SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
+  - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
+  - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
+o verification 1D_ocean_ice_column:
+   made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
+   update results
+o pkg/diagnostics:
+ - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
+   which are not filled-up but computed from other diags ; In this case, the mate
+   diag points to the primary (filled-up) diag to used for post processing.
+ - Update Velocity-potential computation using post-processed diag framework.
+ ==> Change the ordering of fields and time-periods in MDS output file
+   when using periodic averaging: now writes one time record with the full set
+   of fields for this time period, then the next time reccord (it used to be
+   one field with the full set of time records then the next field).
+     Note: this is now similar to NetCDF (MNC) output file. <==
+
+checkpoint62z (2011/06/21)
+o adjoint monitor:
+ - Add adjoint monitor output for packages exf, seaice
+   and update relevant testreport output
+o pkg/seaice:
+ - re-order diags inits so that they appear in order in available_diagnostics.log
+ - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
+   area/heff/hsnow preceeding thermodynamic growth/melt.
+ - modified diag: SIdA; output actual effect, as the description states.
+ - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
+ - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
+   (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
+    and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
+ - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
+ - added diagnostics for seaice generic tracers (SItr*).
+ - added SItrUnit and SItrNameLong run time param (for SItr* diags).
+ - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
+ I. Fenty: 18-Jun-2011:
+ Minor changes to seaice package:
+ 1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
+    added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
+   - Differentiated "regularization variables" from "floor variables"
+    * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
+    * hiceMin became SEAICE_hice_reg (old hiceMin)
+      (with _reg meaning regularization variable)
+   - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
+    so as to ensure energy conservation when going between phases
+  - A22 was not used anywhere
+ 2) Changed regularization procedure for heffActual and hsnowActual to ensure
+    well-boundedness and smooth adjoint in seaice_growth.F
+ 3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
+    because the old regularization always set heffActual >= 0.05 cm
+ 4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
+    on AREA when HEFF > 0.
+  - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
+    requiring that DISABLE_AREA_FLOOR *not* be defined
+ Affected verifications:
+  - 1D_ocean_ice_column (output.txt output_adm.txt)
+  - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
+o pkg/diagnostics:
+  - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
+  - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
+    (was _RL, now integer) with option = 0 to retrieve all levels.
+  - add pieces of code to compute velocity potential at each level (new diagnostics
+    PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
+    for now, using same params as CG2D (target-resisual, max Nb of iter ...).
+  - fix few issues with counter diagnostics in diagnostics_setdiag.F &
+    diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
+    and in diagnostics_fract_fill.F (do not need a valid pointer for the
+    diagnostics counter-mate); check that definition of counter-diagnostic
+    includes a valid counter-mate (in diagnostics_set_levels.F).
+o model/src (rStar):
+  - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
+    affect solution only if z* with full pressure in EOS;
+    update output of test-exp global_ocean.90x40x15.
+o pkg/seaice:
+  - introduce siEps=1e-5 parameter
+  - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
+  - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
+  - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
+    For now it covers, and was tested for, ice salinity and age (attached to HEFF),
+    as well as ice cover age and ridging index (attached to AREA).
+    For now the run time parameters (in data.seaice/SEAICE_PARM03) are
+    SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
+    Up to SItrMaxNum=3 tracers can be used simultaneously.
+o pkg/salt_plume:
+  -introduce SPsalFRAC run time parameter that sets the fraction of the
+   salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
+   that gets vertically redistributed (fluxed down) by pkg/salt_plume.
+o model debug options:
+  - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
+    in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
+  - Refine debug-msg printing selection (3 new levels):
+    debugMode  : controls printing of debug messages (sequence of S/R calls).
+    debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
+     debLevZero =  0 ; /* level of disabled aux. msg printing */
+     debLevA =  1 ; /* level of minimum  aux. msg printing */
+     debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
+     debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
+     debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
+     debLevE =  5 ; /* level of extensive debug printing */
+    New debugLevel default: with default debugMode value (=F),
+      = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
+      and if debugMode=T, default debugLevel = 4 (debLevD).
+    Relation with previous settings:
+     debLevB (=2) corresponds to former debLevA (=1)
+     debLevD (=4) corresponds to former debLevB (=2)
+    Note:
+     a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
+     b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
+        to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
+  - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
+    detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
+o pkg/obcs:
+  - change OBCSfixTopo default from True to False (should not change the results);
+    keep OBCSfixTopo=T in verification-exp. seaice_obcs.
+o pkg/thsice:
+  - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
+    2nd layer seaice sublimation (unlikely to happen)
+  - use Interior mask for OBCS in thsice_advection.F (similar to what is
+    done in gad_advection & seaice_advection).
+o adjoint:
+  bug fix spotted by Gael Forget:
+  seaice_advection and thsice_advection still had
+  legacy CPP options to avoid CS corner updates for adjoint
+o pkg/seaice:
+  => Change some of the defaults (2011/05/29):
+     - change SEAICEuseFluxForm default (from False to True)
+     - change DIFF1 default (from 0.004 m/s to 0. m/s)
+     And print warnings if DIFF1 is not set in data.seaice and centered
+      avection scheme is used without any diffusion.
+  also:
+  - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
+  - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
+  - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
+    other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
+    #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
+  update results of test exp.:
+     lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
+         output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
+         output_adm.noseaicedyn (SEAICEuseFluxForm=T)
+     offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
+     seaice_obcs: output (SEAICEuseFluxForm=T)
+  and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
+      for standard fwd & AD lab_sea tests (to keep the same output).
+o pkg/seaice/seaice_growth.F:
+  - use Ian Fenty's capping formulas for actual ice
+  thickness thoughout EVOLUTION branch.
+  - put treatment pathological case #2) in CPP brackets
+  (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
+  - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
+o pkg/seaice:
+  - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
+  pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
+  also pass fac as a param, which can be 1. (to update the tendency
+  field) or the time step (to update the field itself).
+  - seaice_advdiff.F: for multidim, call seaice_diffusion with
+  e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
+  seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
+  - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
+  hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
+o pkg/seaice:
+  diffusion with centered advection scheme (diffus.F & advect.F):
+  - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
+    to just compute the laplacian of input-field.
+  - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
+  - fix flux-form version in diffus.F to conserve tracer.
+  update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
+   machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
+
+checkpoint62y (2011/05/26)
+o pkg/seaice:
+ - seaice_growth.F : in EVOLUTION branch, always include
+   a_QSWbyATM_cover in qnet (as it should be).
+ - verification/global_ocean.cs32x15 : update results accordingly
+   (output.seaice.txt output_adm.seaice.txt).
+o pkg/seaice + obcs:
+ - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
+   equivalent of assuming no tracer gradient outside the OB region.
+   update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
+ - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
+   after changes above);
+ - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
+   only at OB location (instead of over a band of OLx width).
+o pkg/seaice:
+ - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
+   (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
+o pkg/obcs:
+  - split header file "OBCS.h" into 4 separated files:
+    OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
+   Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
+     (contain no conditional statement which depends on OBCS options).
+  - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
+    to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
+o ctrl, cost, grdchk & autodiff pkgs:
+  - make options file more standard (like other {PKG}_OPTIONS.h file but
+    with AD_CONFIG.h); clean-up some of the included header files.
+o pkg/obcs:
+  - do not mask tracer when applying OB (tracer == 0 could generate problems)
+  - apply tracer OB values to tracer field only at OB location (instead of
+    over a band of OLx width)
+  - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
+  - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
+    obcs_apply_tloc.F & obcs_apply_sloc.F
+o obcs in model/src:
+  - call OBCS_APPLY_W only if NonHydrostatic.
+  - call OBCS_APPLY_ETA only if NonLinFreeSurf.
+  - reset dEtaHdt and wVel to zero outside OB interior region ;
+  - leave tracer unchanged outside OB interior region: This has no effect
+    on the solution but just to prevent unrealistic tracer value outside OB.
+  - zero out velocity outside OB interior region: This has no effect on
+    the solution but just to prevent unrealistic velocity outside OB.
+o obcs and non-lin free-surf:
+   move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
+   and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
+   + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
+   this fixes missing EXCH + get consistent eta OB value (+ fix restart).
+   update results of test-exp. exp4(nlfs).
+o exp4 (nlfs) test-exp:
+   use OBC for Eta at Western & Eastern OB (to test prescribing Eta
+   with NonLin-FreeSurf); update output.nlfs.txt
+o obcs and 2d/3d solver norm:
+   use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
+   and outside OB interior region (will allow to place OB further inside the
+   domain). Depending on the domain, can affects cg2d-Norm (previous
+   cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
+   and cg3d-Norm (previous Norm was computed before canceling OB terms),
+   e.g. in tutorial_plume_on_slope.
+  - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
+o pkg rbcs:
+  - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
+  - add capability to apply relaxation to horizontal velocity uVel & vVel.
+o pkg/grdchk: add gradient check for control variable xx_shifwflx
+o pkg/shelfice/shelfice_init_fixed.F
+  fix CPP-flag combinations
+o pkg/seaice: Merge iceage code of Pierre Rampal
+  * update/change/correct ice age calculations
+  * add age updates for pathological cases
+  Probably needs more testing...
+
+checkpoint62x (2011/05/13)
+o pkg/mom_vecinv:
+   high-order vorticity scheme: use interior masks (maskInW & S)
+   to zero-out (outside OB) gradient of vorticity.
+o verification exp.:
+   turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
+   hs94.128x64x5 and seaice_obcs ; update results.
+o pkg/obcs:
+  fix bug in OBeta for YZ sections in obcs_exf_load.F
+o pkg/ctrl, pkg/shelfice, and optim:
+  - add new control variable xx_shifwflx (fresh water flux underneath ice
+    shelves). This is almost as tedious as obcs-ctrl, because the
+    variables needs its own mask.
+  - add a cost function term that penalizes the deviation of xx_shifwflx
+    from the first guess (zero) in analogy to other control variables
+o pkg/shelfice:
+  - start basic adjoint
+o pkg/ctrl:
+  - remove extra 2D field "for good measure" when initializing in
+    ctrl_set_globfld_[xy/xz/yz].F
+  - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
+  - improve error messages in ctrl_set_unpack_*
+o OBC implementation in momentum:
+   use interior masks (maskInC,W & S) in momentum S/R:
+   - multiply divergence, tension and some del^i.u or del^j.v by maskInC
+   - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
+   - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
+   - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
+   Motivation: fix/clean implementation of OBC with biharmonic-viscosity
+    (and also with Leith/Smagorinsky harmonic-viscosity).
+   Update output of experiment dome and exp4 (+nlfs).
+o exp4 test-exp:
+  - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
+    and prescribe time-varying OB (without pkg/exf) for zonal-velocity
+    at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
+    time-varying OB at Western-side for wVel (NonHyd); update output.
+  - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
+    and biharmonic-viscosity ; also use prescribed time varying OB.
+o pkg/obcs:
+  fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
+o model/src:
+  - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
+  - initialise startTime & nIter0 with unlikely values: allows to set one
+    from the other without ambiguity.
+o seaice_obcs test-exp.:
+  add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
+o pkg/obcs:
+  - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
+    no longer needed with maskInC,W,S in pkg/generic_advdiff.
+o pkg/seaice:
+  - retired SEAICE_SALINITY and SEAICE_salinity in favor of
+    SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
+  - fixed bug in the initialization of sea ice salinity variable HSALT
+    in seaice_init_varia.F  (removed dependence on ICE2WATR)
+o fizhi-cs test exp.:
+   switch reference output convention for these 2 non-standard test-exp,
+    from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
+      to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
+   reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
+o model/inc:
+  - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
+    of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
+o pkg/seaice:
+  - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
+o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
+  - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
+    and initial HSALT
+
+checkpoint62w (2011/04/26)
+o pkg/mom_fluxform:
+  - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
+  - use parameter "sideDragFactor" in no-slip BC side-drag part.
+  - update output of exp. global_ocean.90x40x15
+o pkg/mom_vecinv:
+  mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
+o update seaice exp.:
+  use more consistent parameter values (remove "backward compatability only":
+   ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
+  related to thermodynamics seaice. Update output (fwd+AD) of exp.:
+   1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
+o update test-exp global_ocean.90x40x15:
+  o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
+  o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
+  o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
+  o turn on zStar & viscA4 in standard set-up (dir input/)
+    and update output files: output.txt & output.dwnslp.txt
+o new AD-test experiment: obcs_ctrl
+  (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
+o pkg/dic:
+  fix two bugs in handling water vapour pressure in carbonate chemistry
+  and air-sea fluxes. Found by Val Bennington and Galen McKinley
+  (add DIC Option = WATERVAP_BUG to recover old results)
+  update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
+o adding allowInteriorFreezing option to check for water below freezing point
+  at depth and bring the negative heat anomaly to the surface level
+o pkgs _fields_load:
+  - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
+  - use new S/R GET_PERIODIC_INTERVAL in pkgs:
+    bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
+    rbcs to get interpolation weights and time reccord number.
+  - fix multi-threading in aim_fields_load.F
+  - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
+o external_fields_load:
+  new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
+   interpolation weights) to use in a periodic time-series ; do not divide by
+   time-step to convert to integer:
+   - this fixes case where externForcingPeriod is not multiple of time-step
+      (Thanks to Christopher L. Wolfe)
+   - this fixes case where externForcingPeriod is an odd multiple of time-step
+     (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
+  store index of time-record which is currently loaded:
+   - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
+   - needed for the adjoint but not yet used because of extensive recomputations;
+     (to be fixed soon)
+
+checkpoint62v (2011/04/02)
+o verification/1D_ocean_ice_column added to test Ian Fenty's
+  pkg/seaice_growth.F modifications for improving sea ice code differentiability
+o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
+  (new velocity statistics after changing maskInW & maskInS definition)
+o pkg/generic_advdiff with OBCS:
+  use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
+  equivalent to assumption of no tracer gradient outside the OB region.
+  This will affect the results if using obcs+biharmonic diffusion.
+  update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
+o pkg/obcs:
+  change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
+  (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
+  in Interior region. No impact on solution but affects Velocity monitor stats.
+o pkg/ptracers (adjoint)
+  New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
+  tape file for each tracer
+o model/inc/src and pkg/autodiff: add parameters that allow to turn
+  of parts of the adjoint code at run time. For now, there are only
+  useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
+  parameters are set in data.pkg.
+  This is the lazy coward's version of doing this, but still useful for
+  debugging. In order to do it right, everything needs to be moved to
+  pkg/autodiff.
+o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
+  the end; this fixes the adjoint balancing code for open boundaries.
+o pkg/ctrl:
+  - change behavior of xx_${varname}period to be analogous to exf-conventions:
+    xx_${varname}period =   0.,  means time-independent control part
+    xx_${varname}period = -12., means one-year-periodic monthly control part
+  - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
+    clean up ctrl_init a little, remove unused variables
+  - ctrl_init: fixed the handling of the start/endrec for obcs-variables
+  - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
+
+checkpoint62u (2011/03/15)
 o model/src:
   - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
     h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;